From 85e752cac99ac93b6b72da390439975625686d3d Mon Sep 17 00:00:00 2001
From: Egor Sobolev <egor.sobolev@xfel.eu>
Date: Tue, 23 Jul 2024 20:42:34 +0200
Subject: [PATCH] Write detector resolution in crystfel geometry file, fix type
issue for binary mask bitwise operations
---
src/geomtools/__init__.py | 5 +++--
src/geomtools/detector/crystfel_frm.py | 5 +++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/src/geomtools/__init__.py b/src/geomtools/__init__.py
index 3f182b0..7dbf429 100644
--- a/src/geomtools/__init__.py
+++ b/src/geomtools/__init__.py
@@ -1,6 +1,7 @@
from .detector import ( # noqa E401
- assemble_data, get_pixel_positions, pixels_to_image, plot_data_on_detector,
- plot_detector_layout, read_crystfel_geom, write_crystfel_geom)
+ assemble_data, get_detector_shape, get_pixel_positions, pixels_to_image,
+ plot_data_on_detector, plot_detector_layout, read_crystfel_geom,
+ write_crystfel_geom)
from .sfx import ( # noqa E401
avg_pixel_displacement, badpixels_mask, cell_volume, ellipse, extract_cell,
extract_geometry, gauss2d_fit, get_min_bragg_dist, get_peak_position,
diff --git a/src/geomtools/detector/crystfel_frm.py b/src/geomtools/detector/crystfel_frm.py
index 0319151..008ea5f 100644
--- a/src/geomtools/detector/crystfel_frm.py
+++ b/src/geomtools/detector/crystfel_frm.py
@@ -6,7 +6,6 @@ from natsort import natsorted
from .geom import get_detector_shape
-
HEADER_TEMPLATE = """\
; {detector} geometry file written by geomtools
; You may need to edit this file to add:
@@ -45,6 +44,7 @@ def write_crystfel_geom(file, panels, beam, rigid_groups, mask=None):
"""Writes geometry in CrystFEL format in file."""
# header
clen = panels.clen[0]
+ res = panels.res[0]
paths = {}
paths['data'] = (
panels.data[0] if panels.data[0]
@@ -65,7 +65,7 @@ def write_crystfel_geom(file, panels, beam, rigid_groups, mask=None):
path_str = '\n'.join('{} = {} ;'.format(i, j) for i, j in paths.items())
header = HEADER_TEMPLATE.format(
- detector="AGIPD1M", resolution=1/200e-6, frame_dim=0,
+ detector="AGIPD1M", resolution=res, frame_dim=0,
clen=clen, photon_energy=beam["photon_energy"],
adu_per_ev=1, paths=path_str,
)
@@ -162,6 +162,7 @@ def read_crystfel_geom(filename, indexes=dict()):
if mask_file:
with h5py.File(mask_file, "r") as f:
mask = f[mask_path][:]
+ mask = mask.astype(int)
mask = (
(np.bitwise_and(mask, mask_goodbits) != mask_goodbits) |
(np.bitwise_and(mask, mask_badbits) != 0)
--
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